[Biopython-dev] Fw: Re: RNA module contributions

[Michiel de Hoon]

Forgot to forward this to the list.

--- On Mon, 8/31/09, Michiel de Hoon <mjldehoon at yahoo.com> wrote:

> From: Michiel de Hoon <mjldehoon at yahoo.com>
> Subject: Re: [Biopython-dev] RNA module contributions
> To: "Kristian Rother" <krother at rubor.de>
> Date: Monday, August 31, 2009, 9:49 AM
> Hi Kristian,
> 
> As I am working in transcriptomics, I'll be happy to see
> some more RNA modules in Biopython. Thanks!
> Just one comment for now:
> Recent parsers in Biopython use a function rather than a
> class.
> So instead of
> 
> from Bio import ThisOrThatModule
> handle = open("myinputfile")
> parser = ThisOrThatModule.Parser()
> record = parser.parse(handle)
> 
> you would have
> 
> from Bio import ThisOrThatModule
> handle = open("myinputfile")
> record = ThisOrThatModule.read(handle)
> 
> This assumes that myinputfile contains only one record. If
> you have input files with multiple records, you can use
> 
> from Bio import ThisOrThatModule
> handle = open("myinputfile")
> records = ThisOrThatModule.parse(handle)
> 
> where the parse function is a generator function.
> 
> How about the following for the RNA module?
> 
> from Bio import RNA
> handle = open("myinputfile")
> record = RNA.read(handle, format="vienna")
> # or format="bpseq", as appropriate
> 
> where record will be a Bio.RNA.SecStruc object.
> 
> For consistency with other Biopython modules, you might
> also consider to rename Bio.RNA.SecStruc as Bio.RNA.Record.
> On the other hand, the name SecStruc is more informative,
> and maybe some day there will be other kinds of records in
> Bio.RNA.
> 
> Thanks!
> 
> --Michiel.
> 
> --- On Mon, 8/31/09, Kristian Rother <krother at rubor.de>
> wrote:
> 
> > From: Kristian Rother <krother at rubor.de>
> > Subject: [Biopython-dev] RNA module contributions
> > To: "Biopython-Dev Mailing List" <biopython-dev at lists.open-bio.org>
> > Date: Monday, August 31, 2009, 7:19 AM
> > 
> > Hi,
> > 
> > to start work on RNA modules, I'd like to contribute
> some
> > of our tested modules to BioPython. Before I place
> them into
> > my GIT branch, it would be great to get some
> comments:
> > 
> > Bio.RNA.SecStruc
> >    - represents a RNA secondary structures,
> >    - recognizing of SSEs (helix, loop,
> > bulge, junction)
> >    - recognizing pseudoknots
> > 
> > Bio.RNA.ViennaParser     
> >    - parses RNA secondary structures in the
> > Vienna format into SecStruc objects.
> > 
> > Bio.RNA.BpseqParser          -
> > parses RNA secondary structures in the Bpseq format
> into
> > SecStruc objects.
> > 
> > Connected to RNA, but with a wider focus:
> > 
> > Bio.???.ChemicalGroupFinder
> >    - identifies chemical groups (ribose,
> > carboxyl, etc) in a molecule graph (place to be
> defined
> > yet)
> > 
> > There is a contribution from Bjoern Gruening as well:
> > 
> > Bio.PDB.PDBMLParser
> >    - creates PDB.Structure objects from
> > PDB-XML files.
> > 
> > 
> > Comments and suggestions welcome!
> > 
> > Best Regards,
> >    Kristian Rother
> > 
> > 
> > _______________________________________________
> > Biopython-dev mailing list
> > Biopython-dev at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biopython-dev
> > 
> 
> 
> 
>